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Crystal structure of putative aminotransferase (MocR family) (YP_604413.1) from DEINOCOCCUS GEOTHERMALIS DSM 11300 at 2.60 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2000M MgCl2, 20.0000% PEG-8000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.72 α = 90 b = 103.969 β = 112.63 c = 73.815 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.6 30.002 99.3 0.186 0.186 6.7 3 26740 37.056
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 99.9 0.63 0.63 2 3 1988
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT 3D6K 2.6 30.002 26721 1349 99.09 0.226 0.224 0.2292 0.264 0.2728 RANDOM 45.076
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.32 0.45 -0.53 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.433 r_dihedral_angle_3_deg 10.387 r_dihedral_angle_4_deg 8.622 r_dihedral_angle_1_deg 3.242 r_angle_refined_deg 1.476 r_scangle_it 1.458 r_angle_other_deg 1.272 r_scbond_it 1.006 r_mcangle_it 0.493 r_mcbond_it 0.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.433 r_dihedral_angle_3_deg 10.387 r_dihedral_angle_4_deg 8.622 r_dihedral_angle_1_deg 3.242 r_angle_refined_deg 1.476 r_scangle_it 1.458 r_angle_other_deg 1.272 r_scbond_it 1.006 r_mcangle_it 0.493 r_mcbond_it 0.272 r_nbtor_refined 0.139 r_nbd_refined 0.131 r_symmetry_hbond_refined 0.13 r_nbd_other 0.118 r_symmetry_vdw_other 0.08 r_chiral_restr 0.074 r_xyhbond_nbd_refined 0.074 r_symmetry_vdw_refined 0.074 r_nbtor_other 0.067 r_mcbond_other 0.044 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6344 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PHASER phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction